omicverse.alignment.build_phylogeny

omicverse.alignment.build_phylogeny(asvs_fasta, workdir=None, *, mafft_mode='auto', fasttree_model='gtr', gamma=True, mafft_threads=4, fasttree_threads=None, overwrite=False)

Build a phylogenetic tree end-to-end.

Returns {"aligned": ..., "tree": ..., "newick": "<tree-text>", ...}. The newick string has had vsearch’s ;size=N annotations stripped so that ete3 / unifrac can parse tip labels directly.

Parameters:

• asvs_fasta (str)

• workdir (Optional[str] (default: None))

• mafft_mode (str (default: 'auto'))

• fasttree_model (str (default: 'gtr'))

• gamma (bool (default: True))

• mafft_threads (int (default: 4))

• fasttree_threads (Optional[int] (default: None))

• overwrite (bool (default: False))